BatchPrimer3 is a comprehensive web primer design program using Primer3 core program as a major primer design engine to design different types of PCR primers and sequencing primers in a high-through manner. BatchPrimer3 allows users to design several types of primers including generic primers, hybridization oligos, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. A batch input of large number of sequences and a tab-delimited result output greatly facilitates rapid primer design and ordering process.
SEECER is an error correction method that removes errors that are introduced during sequencing. Mismatches, insertion or deletions are removed by creating multiple alignments of reads and building HMMs that are used to decide which reads are be corrected. In the provided reference it is shown that error correction with SEECER improves the downstream analysis, especially RNA de novo assembly.
PepNovo is a de novo sequencing algorithm for MS/MS spectra. PepNovo accepts MS/MS spectra in the following formats: dta,mgf,mzxml. This version of PepNovo is optimized for ion-trap mass spectromtetry that uses CID fragmentation (charges 1-3, dominant b/y ladders).
Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.
Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.